Looks like the add_filter priorities have been changed in Enfold 3.0, try this:

function avia_remove_main_menu_flags(){
remove_filter( ‘wp_nav_menu_items’, ‘avia_append_lang_flags’, 9998, 2 );
remove_filter( ‘avf_fallback_menu_items’, ‘avia_append_lang_flags’, 9998, 2 );
remove_action( ‘avia_meta_header’, ‘avia_wpml_language_switch’, 10);
}
add_action(‘after_setup_theme’,’avia_remove_main_menu_flags’);